Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate BPHYT_RS04815 BPHYT_RS04815 dihydroxy-acid dehydratase
Query= reanno::Smeli:SM_b20890 (579 letters) >FitnessBrowser__BFirm:BPHYT_RS04815 Length = 557 Score = 332 bits (852), Expect = 2e-95 Identities = 211/547 (38%), Positives = 310/547 (56%), Gaps = 23/547 (4%) Query: 27 HRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAERVKRGVYEAGGFPVEF-- 84 +RS G FD +P+IGI N S +TPCNA L+ LA+ + A P F Sbjct: 19 NRSMYYALGYEKADFD-KPMIGIANGHSTITPCNAGLQRLADAAVAAIKGADANPQIFGT 77 Query: 85 PVFSTGESTLRPT---AMMFRNLAAMDVEESIRGNPVDGVVLLGGCDKTTPSLLMGAASV 141 P S G S +++ R + + +E ++G +DGVV++GGCDK P ++G Sbjct: 78 PTISDGMSMGTEGMKYSLVSREVISDCIETCVQGQWMDGVVVIGGCDKNMPGGMIGMLRT 137 Query: 142 DIPAIVVSGGPMLNGKWRGKD---VGSGTAIWQFSEMVKSGEMSLEEFMDAEQGMARSAG 198 ++P+I V GG + G W+G D V S A+ +F+ +G MS E+F EQ S G Sbjct: 138 NVPSIYVYGGTIRPGNWKGTDLTIVSSFEAVGEFT----AGRMSQEDFDGIEQNACPSTG 193 Query: 199 SCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLTGRRIVEMVKEDLKPSDIL 258 SC M TA+TM+S EALGM+L ++ + D + + + R +VE VK+DLKP DI+ Sbjct: 194 SCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLVESVKKDLKPRDIV 253 Query: 259 TKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWDRLGRDVPTIVNLQPSGKY 318 TK++ ENA+ V A GGSTNAVLH LA+A V+ S+DD++R+ + VP I NL+PSG++ Sbjct: 254 TKKSIENAVAVIMATGGSTNAVLHFLAIAHAAEVEWSIDDFERMRKKVPVICNLKPSGQF 313 Query: 319 LMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTI---WNDVKGVVNYNEDVILPREKA 375 + + + AGG+P V+K + + GLLH D IT++G TI DV G ++ VI P ++A Sbjct: 314 VATDLHKAGGIPQVMKILLDAGLLHGDCITITGRTIAEELKDVPGKPRADQQVIFPIDQA 373 Query: 376 LTKSGGIAVLRGNLAPRGAVLKPSAASPHLMQHKGRAVVFESIEDYHARINREDLDIDET 435 L K G +A+L+GNLA GAV K + ++ G A VF+ + I + + + Sbjct: 374 LYKEGHLAILKGNLAVDGAVAKITGLKNPVI--TGPARVFDDEQSALEAILADKIVAGD- 430 Query: 436 CIMVLKYCGPKGYPGMAEVGNMGLPPKVLKKGITDMI-RISDARMSGTAYGTVILHTAPE 494 ++VL+Y GPKG PGM E+ + ++ KG+ + + I+D R SG +G V+ H APE Sbjct: 431 -VVVLRYLGPKGGPGMPEM--LAPTSAIIGKGLGESVGLITDGRFSGGTWGMVVGHVAPE 487 Query: 495 AAEGGPLALVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSPVKPLTGGYGGLYIKTV 554 A GG +A V+ GD I +D L L++ + EL RRRAAW P T G Y Sbjct: 488 AFVGGTIAFVQEGDSITIDAHKLLLQLNIDNAELERRRAAWQQPKPRYTRGVMAKYFALA 547 Query: 555 MQADAGA 561 A+ GA Sbjct: 548 QPANKGA 554 Lambda K H 0.318 0.135 0.402 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 932 Number of extensions: 57 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 579 Length of database: 557 Length adjustment: 36 Effective length of query: 543 Effective length of database: 521 Effective search space: 282903 Effective search space used: 282903 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory